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When a meteorite that contained Deoxys entered the earth's atmosphere, Rayquaza sensed its presence and narrowly avoids the falling rock, angrily roaring at it. Deoxys emerged from the meteorite when it crash landed, but was suddenly attacked by Rayquaza, who believed that Deoxys was invading its territory. After a destructive battle over a glacier witnessed by Professor Lund, Yuko and Lund's son Tory, and although it takes a few Psycho Boosts and is critically hit and falls into the freezing ocean, Rayquaza emerged from the sea and destroyed Deoxys with a Hyper Beam attack at close range. Satisfied with its victory, the Sky High Pokémon returned to the ozone layer.
Four years later, Deoxys manages to regenerate, and it goes to search for its friend, a fellow Deoxys. Rayquaza sensed Deoxys' presence and goes to LaRousse City to battle it again. After LaRousse City has been evacuated because of the Dragon type's arrival there, Rayquaza manages to break through Deoxys's city-wide barrier after many failed attempts, and soon it and Deoxys had a second spectacular battle that destroys some of the city. This time Deoxys gained the upper-hand in the fight and was about to deliver the final blow upon Rayquaza, but was stopped by the arrival of its revived friend. As the two Deoxys reunite, Rayquaza recovers and attacks the two DNA Pokémon, triggering another fight which causes more trouble in the city when Rayquaza blindly fires a Hyper Beam attack within the main power station, causing the security bots to malfunction and flood the streets.
During the battle, Rayquaza becomes engulfed in the sea of malfunctioning security cubes, and the two Deoxys came to protect it by trying to block the incoming onslaught. At that moment, Rayquaza realizes that the Deoxys aren't enemies and stops attacking, but the three were soon overwhelmed by the flood of security bots. When the security bots were shut down to prevent further destruction, Rayquaza emerges from the sea of bots and briefly flies with the two Deoxys, Ash, Tory and Pikachu before returning to the ozone layer on peaceful terms.
|Ice Beam||Destiny Deoxys|
|Hyper Beam||Destiny Deoxys|
|+ indicates this Pokémon used this move recently.*|
- indicates this Pokémon normally can't use this move.